PD

momapy.sbgn.pd

Classes:

Name	Description
AndOperator	Class for and operators
AndOperatorLayout	Class for and operator layouts
Association	Class for associations
AssociationLayout	Class for association layouts
CardinalityLayout	Class for cardinality layouts
Catalysis	Class for catalyses
CatalysisLayout	Class for catalysis layouts
Compartment	Class for compartments
CompartmentLayout	Class for compartment layouts
Complex	Class for complexes
ComplexLayout	Class for complex layouts
ComplexMultimer	Class for complex multimers
ComplexMultimerLayout	Class for complex multimer layouts
ComplexMultimerSubunit	Class for complex subunits
ComplexMultimerSubunitLayout	Class for complex multimer subunit layouts
ComplexSubunit	Class for complex subunits
ComplexSubunitLayout	Class for complex subunit layouts
ConsumptionLayout	Class for consumption layouts
Dissociation	Class for dissociations
DissociationLayout	Class for dissociation layouts
EmptySet	Class for empty sets
EmptySetLayout	Class for empty set layouts
EntityPool	Base class for entity pools
EquivalenceArcLayout	Class for equivalence arc layouts
EquivalenceOperator	Class for equivalence operators
EquivalenceOperatorInput	Class for inputs of equivalence operators
EquivalenceOperatorLayout	Class for equivalence operator layouts
EquivalenceOperatorOutput	Class for outputs of equivalence operators
FluxRole	Base class for flux roles
GenericProcess	Class for generic processes
GenericProcessLayout	Class for generic process layouts
Inhibition	Class for inhibitions
InhibitionLayout	Class for inhibition layouts
LogicArcLayout	Class for logic arc layouts
LogicalOperator	Class for logical operators
LogicalOperatorInput	Class for inputs of logical operators
Macromolecule	Class for macromolecules
MacromoleculeLayout	Class for macromolecule layouts
MacromoleculeMultimer	Class for macromolecule multimers
MacromoleculeMultimerLayout	Class for macromolecule multimer layouts
MacromoleculeMultimerSubunit	Class for macromolecule multimer subunits
MacromoleculeMultimerSubunitLayout	Class for macromolecule multimer subunit layouts
MacromoleculeSubunit	Class for macromolecule subunits
MacromoleculeSubunitLayout	Class for macromolecule subunit layouts
Modulation	Class for modulations
ModulationLayout	Class for modulation layouts
Multimer	Base class for multimers
MultimerSubunit	Base class for multimer subunits
NecessaryStimulation	Class for necessary stimulations
NecessaryStimulationLayout	Class for necessary stimulation layouts
NotOperator	Class for not operators
NotOperatorLayout	Class for not operator layouts
NucleicAcidFeature	Class for nucleic acid features
NucleicAcidFeatureLayout	Class for nucleic acid feature layouts
NucleicAcidFeatureMultimer	Class for nucleic acid feature multimers
NucleicAcidFeatureMultimerLayout	Class for nucleic acid feature multimer layouts
NucleicAcidFeatureMultimerSubunit	Class for nucleic acid feature multimer subunits
NucleicAcidFeatureMultimerSubunitLayout	Class for nucleic acid feature multimer subunit layouts
NucleicAcidFeatureSubunit	Class for nucleic acid feature subunits
NucleicAcidFeatureSubunitLayout	Class for nucleic acid feature subunit layouts
OmittedProcess	Class for omitted processes
OmittedProcessLayout	Class for omitted process layouts
OrOperator	Class for or operators
OrOperatorLayout	Class for or operator layouts
PerturbingAgent	Class for perturbing agents
PerturbingAgentLayout	Class for perturbing agent layouts
Phenotype	Class for phenotypes
PhenotypeLayout	Class for phenotype layouts
Process	Base class for processes
Product	Class for products
ProductionLayout	Class for production layouts
Reactant	Class for reactants
SBGNPDLayout	Class for SBGN-PD layouts
SBGNPDMap	Class for SBGN-PD maps
SBGNPDModel	Class for SBGN-PD models
SimpleChemical	Class for simple chemical
SimpleChemicalLayout	Class for simple chemical layouts
SimpleChemicalMultimer	Class for simple chemical multimers
SimpleChemicalMultimerLayout	Class for simple chemical multimer layouts
SimpleChemicalMultimerSubunit	Class for simple chemical multimer subunits
SimpleChemicalMultimerSubunitLayout	Class for simple chemical multimer subunit layouts
SimpleChemicalSubunit	Class for simple chemical subunits
SimpleChemicalSubunitLayout	Class for simple chemical subunit layouts
StateVariable	Class for state variables
StateVariableLayout	Class for state variable layouts
Stimulation	Class for stimulations
StimulationLayout	Class for stimulation layouts
StoichiometricProcess	Base class for stoichiometric processes
Submap	Class for submaps
SubmapLayout	Class for submap layouts
Subunit	Base class for subunits
Tag	Class for tags
TagLayout	Class for tag layouts
TagReference	Class for tag references
Terminal	Class for terminals
TerminalLayout	Class for terminal layouts
TerminalReference	Class for terminal references
UncertainProcess	Class for uncertain processes
UncertainProcessLayout	Class for uncertain process layouts
UnitOfInformation	Class for units of information
UnitOfInformationLayout	Class for unit of information layouts
UnspecifiedEntity	Class for unspecified entities
UnspecifiedEntityLayout	Class for unspecified entity layouts
UnspecifiedEntitySubunit	Class for unspecified entity subunits
UnspecifiedEntitySubunitLayout	Class for unspecified entity subunit layouts

Attributes:

Name	Type	Description
SBGNPDLayoutBuilder		Class for SBGN-PD layout builders
SBGNPDMapBuilder		Class for SBGN-PD map builders
SBGNPDModelBuilder		Class for SBGN-PD model builders

AndOperator dataclass

AndOperator(
    *,
    id_: str = get_uuid4_as_str(),
    inputs: frozenset[LogicalOperatorInput] = frozenset()
)

Bases: LogicalOperator

Class for and operators

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'7d28b4d6-06c8-4352-9c1a-c68bca8a9f8c'

AndOperatorLayout dataclass

AndOperatorLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 30.0,
    direction: Direction = HORIZONTAL,
    left_to_right: bool = True,
    left_connector_length: float = 10.0,
    right_connector_length: float = 10.0,
    left_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    left_connector_stroke_width: float | None = None,
    left_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    left_connector_stroke_dashoffset: float | None = None,
    left_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    left_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    left_connector_filter: (
        NoneValueType | Filter | None
    ) = None,
    right_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    right_connector_stroke_width: float | None = None,
    right_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    right_connector_stroke_dashoffset: float | None = None,
    right_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    right_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    right_connector_filter: (
        NoneValueType | Filter | None
    ) = None
)

Bases: _ConnectorsMixin, _SimpleMixin, _TextMixin, SBGNNode

Class for and operator layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'092140f1-d606-49ee-bf93-db3056701771'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		30.0
direction	Direction		<Direction.HORIZONTAL: 1>
left_to_right	bool		True
left_connector_length	float		10.0
right_connector_length	float		10.0
left_connector_stroke	NoneValueType | Color | None		None
left_connector_stroke_width	float | None		None
left_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
left_connector_stroke_dashoffset	float | None		None
left_connector_fill	NoneValueType | Color | None		None
left_connector_transform	NoneValueType | tuple[Transformation] | None		None
left_connector_filter	NoneValueType | Filter | None		None
right_connector_stroke	NoneValueType | Color | None		None
right_connector_stroke_width	float | None		None
right_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
right_connector_stroke_dashoffset	float | None		None
right_connector_fill	NoneValueType | Color | None		None
right_connector_transform	NoneValueType | tuple[Transformation] | None		None
right_connector_filter	NoneValueType | Filter | None		None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Association dataclass

Association(
    *,
    id_: str = get_uuid4_as_str(),
    reactants: frozenset[Reactant] = frozenset(),
    products: frozenset[Product] = frozenset(),
    reversible: bool = False
)

Bases: GenericProcess

Class for associations

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'50b13b0f-b89e-48bb-8ef4-2140afe8963a'
reversible	bool		False

AssociationLayout dataclass

AssociationLayout(
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    fill: NoneValueType | Color | None = black,
    filter: NoneValueType | Filter | None = None,
    height: float = 20.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 20.0,
    direction: Direction = HORIZONTAL,
    left_to_right: bool = True,
    left_connector_length: float = 10.0,
    right_connector_length: float = 10.0,
    left_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    left_connector_stroke_width: float | None = None,
    left_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    left_connector_stroke_dashoffset: float | None = None,
    left_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    left_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    left_connector_filter: (
        NoneValueType | Filter | None
    ) = None,
    right_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    right_connector_stroke_width: float | None = None,
    right_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    right_connector_stroke_dashoffset: float | None = None,
    right_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    right_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    right_connector_filter: (
        NoneValueType | Filter | None
    ) = None
)

Bases: _ConnectorsMixin, _SimpleMixin, SBGNNode

Class for association layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'104f50e9-d889-497b-839e-2f1c8d732791'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		20.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		20.0
direction	Direction		<Direction.HORIZONTAL: 1>
left_to_right	bool		True
left_connector_length	float		10.0
right_connector_length	float		10.0
left_connector_stroke	NoneValueType | Color | None		None
left_connector_stroke_width	float | None		None
left_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
left_connector_stroke_dashoffset	float | None		None
left_connector_fill	NoneValueType | Color | None		None
left_connector_transform	NoneValueType | tuple[Transformation] | None		None
left_connector_filter	NoneValueType | Filter | None		None
right_connector_stroke	NoneValueType | Color | None		None
right_connector_stroke_width	float | None		None
right_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
right_connector_stroke_dashoffset	float | None		None
right_connector_fill	NoneValueType | Color | None		None
right_connector_transform	NoneValueType | tuple[Transformation] | None		None
right_connector_filter	NoneValueType | Filter | None		None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

CardinalityLayout dataclass

CardinalityLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 19.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 12.0
)

Bases: _SimpleMixin, SBGNNode

Class for cardinality layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'7bf5f910-f1da-47a1-a660-571bdce338fd'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		19.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		12.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Catalysis dataclass

Catalysis(
    *,
    id_: str = get_uuid4_as_str(),
    source: EntityPool | LogicalOperator,
    target: Process
)

Bases: Stimulation

Class for catalyses

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'fdf477d5-0f80-4787-b284-65ac2076a3e1'
source	EntityPool | LogicalOperator		required
target	Process		required

CatalysisLayout dataclass

CatalysisLayout(
    path_fill: NoneValueType | Color | None = NoneValue,
    path_stroke: NoneValueType | Color | None = black,
    path_stroke_width: float | None = 1.25,
    arrowhead_fill: NoneValueType | Color | None = white,
    arrowhead_stroke: NoneValueType | Color | None = black,
    arrowhead_stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    end_shorten: float = 0.0,
    fill: NoneValueType | Color | None = None,
    filter: NoneValueType | Filter | None = None,
    path_filter: NoneValueType | Filter | None = None,
    path_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    path_stroke_dashoffset: float | None = None,
    path_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    stroke: NoneValueType | Color | None = None,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    stroke_width: float | None = None,
    segments: tuple[
        Segment | BezierCurve | EllipticalArc
    ] = tuple(),
    source: LayoutElement | None = None,
    start_shorten: float = 0.0,
    target: LayoutElement | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_filter: NoneValueType | Filter | None = None,
    arrowhead_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    arrowhead_stroke_dashoffset: float | None = None,
    arrowhead_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_height: float = 10.0,
    arrowhead_width: float = 10.0
)

Bases: SBGNSingleHeadedArc

Class for catalysis layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'83dcf0eb-98b0-4329-8e4e-b09a02d83248'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter	NoneValueType | Filter | None	The fill filter of the arc	None
path_fill	NoneValueType | Color | None		<momapy.drawing.NoneValueType object at 0x7f3954141040>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None		1.25
path_transform	NoneValueType | tuple[Transformation] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the arc	None
stroke_dashoffset	float | None	The stroke dashoffset of the arc	None
stroke_width	float | None	The stroke width of the arc	None
segments	tuple[Union[Segment, BezierCurve, EllipticalArc]]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None		1.25
arrowhead_transform	NoneValueType | tuple[Transformation] | None	The arrowhead transform of the arc	None
arrowhead_height	float		10.0
arrowhead_width	float		10.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=elements,
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=actions,
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

Compartment dataclass

Compartment(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset()
)

Bases: SBGNModelElement

Class for compartments

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'639ded38-cfeb-48aa-8e68-18e49a3fa508'
label	str | None		None

CompartmentLayout dataclass

CompartmentLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 80.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    stroke_width: float = 3.25,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 80.0,
    rounded_corners: float = 5.0
)

Bases: _SimpleMixin, SBGNNode

Class for compartment layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'8a67ae85-87df-4f92-b2e7-cf4f53cdfd4e'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		80.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float		3.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		80.0
rounded_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Complex dataclass

Complex(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None,
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset(),
    subunits: frozenset[Subunit] = frozenset()
)

Bases: EntityPool

Class for complexes

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'56d51f68-4c00-4951-b54d-b5d3efa82cf0'
compartment	Compartment | None		None
label	str | None		None

ComplexLayout dataclass

ComplexLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 44.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 44.0,
    cut_corners: float = 5.0
)

Bases: _SimpleMixin, SBGNNode

Class for complex layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'269ad92a-6c7d-41b9-82dd-55a3b57a2266'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		44.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		44.0
cut_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

ComplexMultimer dataclass

ComplexMultimer(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None,
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset(),
    subunits: frozenset[Subunit] = frozenset(),
    cardinality: int | None = None
)

Bases: Multimer

Class for complex multimers

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'bf04663a-fecb-47c5-b229-72be84e9ec1b'
compartment	Compartment | None		None
label	str | None		None
cardinality	int | None		None

ComplexMultimerLayout dataclass

ComplexMultimerLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    offset: float = 3.0,
    subunits_stroke: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_stroke_width: (
        tuple[NoneValueType | float] | None
    ) = None,
    subunits_stroke_dasharray: (
        tuple[NoneValueType | tuple[float]] | None
    ) = None,
    subunits_stroke_dashoffset: tuple[float] | None = None,
    subunits_fill: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_transform: (
        tuple[NoneValueType | tuple[Transformation]] | None
    ) = None,
    subunits_filter: (
        tuple[NoneValueType | Filter] | None
    ) = None,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 44.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 44.0,
    cut_corners: float = 5.0
)

Bases: _MultiMixin, SBGNNode

Class for complex multimer layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'add150dd-d267-4c7e-a8ae-f27f232e483d'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		44.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		44.0
offset	float		3.0
subunits_stroke	tuple[Union[NoneValueType, Color]] | None		None
subunits_stroke_width	tuple[Union[NoneValueType, float]] | None		None
subunits_stroke_dasharray	tuple[Union[NoneValueType, tuple[float]]] | None		None
subunits_stroke_dashoffset	tuple[float] | None		None
subunits_fill	tuple[Union[NoneValueType, Color]] | None		None
subunits_transform	tuple[Union[NoneValueType, tuple[Transformation]]] | None		None
subunits_filter	tuple[Union[NoneValueType, Filter]] | None		None
cut_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

ComplexMultimerSubunit dataclass

ComplexMultimerSubunit(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset(),
    subunits: frozenset[Subunit] = frozenset(),
    cardinality: int | None = None
)

Bases: MultimerSubunit

Class for complex subunits

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'4cf4d117-b711-4743-9964-9a674e49e2c6'
label	str | None		None
cardinality	int | None		None

ComplexMultimerSubunitLayout dataclass

ComplexMultimerSubunitLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    offset: float = 3.0,
    subunits_stroke: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_stroke_width: (
        tuple[NoneValueType | float] | None
    ) = None,
    subunits_stroke_dasharray: (
        tuple[NoneValueType | tuple[float]] | None
    ) = None,
    subunits_stroke_dashoffset: tuple[float] | None = None,
    subunits_fill: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_transform: (
        tuple[NoneValueType | tuple[Transformation]] | None
    ) = None,
    subunits_filter: (
        tuple[NoneValueType | Filter] | None
    ) = None,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0,
    cut_corners: float = 5.0
)

Bases: _MultiMixin, SBGNNode

Class for complex multimer subunit layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'ed28b093-01c3-4f62-82ce-a384ef7c58fe'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
offset	float		3.0
subunits_stroke	tuple[Union[NoneValueType, Color]] | None		None
subunits_stroke_width	tuple[Union[NoneValueType, float]] | None		None
subunits_stroke_dasharray	tuple[Union[NoneValueType, tuple[float]]] | None		None
subunits_stroke_dashoffset	tuple[float] | None		None
subunits_fill	tuple[Union[NoneValueType, Color]] | None		None
subunits_transform	tuple[Union[NoneValueType, tuple[Transformation]]] | None		None
subunits_filter	tuple[Union[NoneValueType, Filter]] | None		None
cut_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

ComplexSubunit dataclass

ComplexSubunit(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset(),
    subunits: frozenset[Subunit] = frozenset()
)

Bases: Subunit

Class for complex subunits

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'32c40c61-954f-456b-b295-29de6a9887e7'
label	str | None		None

ComplexSubunitLayout dataclass

ComplexSubunitLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0,
    cut_corners: float = 5.0
)

Bases: _SimpleMixin, SBGNNode

Class for complex subunit layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'5f351a2b-e5cc-456f-b365-b07b06634ccb'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
cut_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

ConsumptionLayout dataclass

ConsumptionLayout(
    path_fill: NoneValueType | Color | None = NoneValue,
    path_stroke: NoneValueType | Color | None = black,
    path_stroke_width: float | None = 1.25,
    arrowhead_fill: NoneValueType | Color | None = white,
    arrowhead_stroke: NoneValueType | Color | None = black,
    arrowhead_stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    end_shorten: float = 0.0,
    fill: NoneValueType | Color | None = None,
    filter: NoneValueType | Filter | None = None,
    path_filter: NoneValueType | Filter | None = None,
    path_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    path_stroke_dashoffset: float | None = None,
    path_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    stroke: NoneValueType | Color | None = None,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    stroke_width: float | None = None,
    segments: tuple[
        Segment | BezierCurve | EllipticalArc
    ] = tuple(),
    source: LayoutElement | None = None,
    start_shorten: float = 0.0,
    target: LayoutElement | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_filter: NoneValueType | Filter | None = None,
    arrowhead_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    arrowhead_stroke_dashoffset: float | None = None,
    arrowhead_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None
)

Bases: SBGNSingleHeadedArc

Class for consumption layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'd795cd71-8be1-4328-912c-c83970ff3bf8'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter	NoneValueType | Filter | None	The fill filter of the arc	None
path_fill	NoneValueType | Color | None		<momapy.drawing.NoneValueType object at 0x7f3954141040>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None		1.25
path_transform	NoneValueType | tuple[Transformation] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the arc	None
stroke_dashoffset	float | None	The stroke dashoffset of the arc	None
stroke_width	float | None	The stroke width of the arc	None
segments	tuple[Union[Segment, BezierCurve, EllipticalArc]]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None		1.25
arrowhead_transform	NoneValueType | tuple[Transformation] | None	The arrowhead transform of the arc	None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=elements,
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=actions,
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

Dissociation dataclass

Dissociation(
    *,
    id_: str = get_uuid4_as_str(),
    reactants: frozenset[Reactant] = frozenset(),
    products: frozenset[Product] = frozenset(),
    reversible: bool = False
)

Bases: GenericProcess

Class for dissociations

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'205b8641-3f48-41cb-a97b-04c3af5e447c'
reversible	bool		False

DissociationLayout dataclass

DissociationLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 20.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 20.0,
    direction: Direction = HORIZONTAL,
    left_to_right: bool = True,
    left_connector_length: float = 10.0,
    right_connector_length: float = 10.0,
    left_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    left_connector_stroke_width: float | None = None,
    left_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    left_connector_stroke_dashoffset: float | None = None,
    left_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    left_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    left_connector_filter: (
        NoneValueType | Filter | None
    ) = None,
    right_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    right_connector_stroke_width: float | None = None,
    right_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    right_connector_stroke_dashoffset: float | None = None,
    right_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    right_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    right_connector_filter: (
        NoneValueType | Filter | None
    ) = None,
    sep: float = 3.0
)

Bases: _ConnectorsMixin, _SimpleMixin, SBGNNode

Class for dissociation layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'53a0873d-d36c-4189-ab2a-92060107a93b'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		20.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		20.0
direction	Direction		<Direction.HORIZONTAL: 1>
left_to_right	bool		True
left_connector_length	float		10.0
right_connector_length	float		10.0
left_connector_stroke	NoneValueType | Color | None		None
left_connector_stroke_width	float | None		None
left_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
left_connector_stroke_dashoffset	float | None		None
left_connector_fill	NoneValueType | Color | None		None
left_connector_transform	NoneValueType | tuple[Transformation] | None		None
left_connector_filter	NoneValueType | Filter | None		None
right_connector_stroke	NoneValueType | Color | None		None
right_connector_stroke_width	float | None		None
right_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
right_connector_stroke_dashoffset	float | None		None
right_connector_fill	NoneValueType | Color | None		None
right_connector_transform	NoneValueType | tuple[Transformation] | None		None
right_connector_filter	NoneValueType | Filter | None		None
sep	float		3.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

EmptySet dataclass

EmptySet(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None
)

Bases: EntityPool

Class for empty sets

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'800e7c54-a8d3-42e0-a8f0-49081f36a295'
compartment	Compartment | None		None

EmptySetLayout dataclass

EmptySetLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 22.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 22.0
)

Bases: _SimpleMixin, SBGNNode

Class for empty set layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'12de1bd3-7c84-4d98-9977-24e05d6efc67'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		22.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		22.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

EntityPool dataclass

EntityPool(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None
)

Bases: SBGNModelElement

Base class for entity pools

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'1cbfe59a-01e5-4467-a980-9eb2a716efdd'
compartment	Compartment | None		None

EquivalenceArcLayout dataclass

EquivalenceArcLayout(
    path_fill: NoneValueType | Color | None = NoneValue,
    path_stroke: NoneValueType | Color | None = black,
    path_stroke_width: float | None = 1.25,
    arrowhead_fill: NoneValueType | Color | None = white,
    arrowhead_stroke: NoneValueType | Color | None = black,
    arrowhead_stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    end_shorten: float = 0.0,
    fill: NoneValueType | Color | None = None,
    filter: NoneValueType | Filter | None = None,
    path_filter: NoneValueType | Filter | None = None,
    path_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    path_stroke_dashoffset: float | None = None,
    path_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    stroke: NoneValueType | Color | None = None,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    stroke_width: float | None = None,
    segments: tuple[
        Segment | BezierCurve | EllipticalArc
    ] = tuple(),
    source: LayoutElement | None = None,
    start_shorten: float = 0.0,
    target: LayoutElement | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_filter: NoneValueType | Filter | None = None,
    arrowhead_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    arrowhead_stroke_dashoffset: float | None = None,
    arrowhead_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None
)

Bases: SBGNSingleHeadedArc

Class for equivalence arc layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'2fc7ee4a-fb97-4de7-bc25-fb42019790e0'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter	NoneValueType | Filter | None	The fill filter of the arc	None
path_fill	NoneValueType | Color | None		<momapy.drawing.NoneValueType object at 0x7f3954141040>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None		1.25
path_transform	NoneValueType | tuple[Transformation] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the arc	None
stroke_dashoffset	float | None	The stroke dashoffset of the arc	None
stroke_width	float | None	The stroke width of the arc	None
segments	tuple[Union[Segment, BezierCurve, EllipticalArc]]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None		1.25
arrowhead_transform	NoneValueType | tuple[Transformation] | None	The arrowhead transform of the arc	None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=elements,
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=actions,
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

EquivalenceOperator dataclass

EquivalenceOperator(
    *,
    id_: str = get_uuid4_as_str(),
    inputs: frozenset[
        EquivalenceOperatorInput
    ] = frozenset(),
    output: EquivalenceOperatorOutput | None = None
)

Bases: SBGNModelElement

Class for equivalence operators

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'2abb0f21-fb66-490a-b925-8fa859c30cb7'
output	EquivalenceOperatorOutput | None		None

EquivalenceOperatorInput dataclass

EquivalenceOperatorInput(
    *, id_: str = get_uuid4_as_str(), element: EntityPool
)

Bases: SBGNRole

Class for inputs of equivalence operators

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'5e3acb64-a6db-4bb4-82fd-a1fb3702c493'
element	EntityPool		required

EquivalenceOperatorLayout dataclass

EquivalenceOperatorLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 30.0,
    direction: Direction = HORIZONTAL,
    left_to_right: bool = True,
    left_connector_length: float = 10.0,
    right_connector_length: float = 10.0,
    left_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    left_connector_stroke_width: float | None = None,
    left_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    left_connector_stroke_dashoffset: float | None = None,
    left_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    left_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    left_connector_filter: (
        NoneValueType | Filter | None
    ) = None,
    right_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    right_connector_stroke_width: float | None = None,
    right_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    right_connector_stroke_dashoffset: float | None = None,
    right_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    right_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    right_connector_filter: (
        NoneValueType | Filter | None
    ) = None
)

Bases: _ConnectorsMixin, _SimpleMixin, _TextMixin, SBGNNode

Class for equivalence operator layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'504616bb-9e9e-41ba-b4be-29db28feb025'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		30.0
direction	Direction		<Direction.HORIZONTAL: 1>
left_to_right	bool		True
left_connector_length	float		10.0
right_connector_length	float		10.0
left_connector_stroke	NoneValueType | Color | None		None
left_connector_stroke_width	float | None		None
left_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
left_connector_stroke_dashoffset	float | None		None
left_connector_fill	NoneValueType | Color | None		None
left_connector_transform	NoneValueType | tuple[Transformation] | None		None
left_connector_filter	NoneValueType | Filter | None		None
right_connector_stroke	NoneValueType | Color | None		None
right_connector_stroke_width	float | None		None
right_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
right_connector_stroke_dashoffset	float | None		None
right_connector_fill	NoneValueType | Color | None		None
right_connector_transform	NoneValueType | tuple[Transformation] | None		None
right_connector_filter	NoneValueType | Filter | None		None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

EquivalenceOperatorOutput dataclass

EquivalenceOperatorOutput(
    *, id_: str = get_uuid4_as_str(), element: EntityPool
)

Bases: SBGNRole

Class for outputs of equivalence operators

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'2563d2ae-ce40-4bef-bd5a-0b32fcfb5d96'
element	EntityPool		required

FluxRole dataclass

FluxRole(
    *,
    id_: str = get_uuid4_as_str(),
    element: EntityPool,
    stoichiometry: int | None = None
)

Bases: SBGNRole

Base class for flux roles

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'0513cf04-2f7d-44bb-8d31-e8571763a8cb'
element	EntityPool		required
stoichiometry	int | None		None

GenericProcess dataclass

GenericProcess(
    *,
    id_: str = get_uuid4_as_str(),
    reactants: frozenset[Reactant] = frozenset(),
    products: frozenset[Product] = frozenset(),
    reversible: bool = False
)

Bases: StoichiometricProcess

Class for generic processes

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'cba11dae-8ce5-4ab3-acbb-d0ed19f35a06'
reversible	bool		False

GenericProcessLayout dataclass

GenericProcessLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 20.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 20.0,
    direction: Direction = HORIZONTAL,
    left_to_right: bool = True,
    left_connector_length: float = 10.0,
    right_connector_length: float = 10.0,
    left_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    left_connector_stroke_width: float | None = None,
    left_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    left_connector_stroke_dashoffset: float | None = None,
    left_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    left_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    left_connector_filter: (
        NoneValueType | Filter | None
    ) = None,
    right_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    right_connector_stroke_width: float | None = None,
    right_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    right_connector_stroke_dashoffset: float | None = None,
    right_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    right_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    right_connector_filter: (
        NoneValueType | Filter | None
    ) = None
)

Bases: _ConnectorsMixin, _SimpleMixin, SBGNNode

Class for generic process layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'397ca594-b856-48e1-ab96-372d19b1e53c'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		20.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		20.0
direction	Direction		<Direction.HORIZONTAL: 1>
left_to_right	bool		True
left_connector_length	float		10.0
right_connector_length	float		10.0
left_connector_stroke	NoneValueType | Color | None		None
left_connector_stroke_width	float | None		None
left_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
left_connector_stroke_dashoffset	float | None		None
left_connector_fill	NoneValueType | Color | None		None
left_connector_transform	NoneValueType | tuple[Transformation] | None		None
left_connector_filter	NoneValueType | Filter | None		None
right_connector_stroke	NoneValueType | Color | None		None
right_connector_stroke_width	float | None		None
right_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
right_connector_stroke_dashoffset	float | None		None
right_connector_fill	NoneValueType | Color | None		None
right_connector_transform	NoneValueType | tuple[Transformation] | None		None
right_connector_filter	NoneValueType | Filter | None		None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Inhibition dataclass

Inhibition(
    *,
    id_: str = get_uuid4_as_str(),
    source: EntityPool | LogicalOperator,
    target: Process
)

Bases: Modulation

Class for inhibitions

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'e2eb747d-4c04-4867-a920-fbdc21d64027'
source	EntityPool | LogicalOperator		required
target	Process		required

InhibitionLayout dataclass

InhibitionLayout(
    path_fill: NoneValueType | Color | None = NoneValue,
    path_stroke: NoneValueType | Color | None = black,
    path_stroke_width: float | None = 1.25,
    arrowhead_fill: NoneValueType | Color | None = white,
    arrowhead_stroke: NoneValueType | Color | None = black,
    arrowhead_stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    end_shorten: float = 0.0,
    fill: NoneValueType | Color | None = None,
    filter: NoneValueType | Filter | None = None,
    path_filter: NoneValueType | Filter | None = None,
    path_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    path_stroke_dashoffset: float | None = None,
    path_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    stroke: NoneValueType | Color | None = None,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    stroke_width: float | None = None,
    segments: tuple[
        Segment | BezierCurve | EllipticalArc
    ] = tuple(),
    source: LayoutElement | None = None,
    start_shorten: float = 0.0,
    target: LayoutElement | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_filter: NoneValueType | Filter | None = None,
    arrowhead_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    arrowhead_stroke_dashoffset: float | None = None,
    arrowhead_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_height: float = 10.0
)

Bases: SBGNSingleHeadedArc

Class for inhibition layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'1532d04f-8f6a-4c62-87cb-d3e2c90a76eb'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter	NoneValueType | Filter | None	The fill filter of the arc	None
path_fill	NoneValueType | Color | None		<momapy.drawing.NoneValueType object at 0x7f3954141040>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None		1.25
path_transform	NoneValueType | tuple[Transformation] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the arc	None
stroke_dashoffset	float | None	The stroke dashoffset of the arc	None
stroke_width	float | None	The stroke width of the arc	None
segments	tuple[Union[Segment, BezierCurve, EllipticalArc]]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None		1.25
arrowhead_transform	NoneValueType | tuple[Transformation] | None	The arrowhead transform of the arc	None
arrowhead_height	float		10.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=elements,
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=actions,
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

LogicArcLayout dataclass

LogicArcLayout(
    path_fill: NoneValueType | Color | None = NoneValue,
    path_stroke: NoneValueType | Color | None = black,
    path_stroke_width: float | None = 1.25,
    arrowhead_fill: NoneValueType | Color | None = white,
    arrowhead_stroke: NoneValueType | Color | None = black,
    arrowhead_stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    end_shorten: float = 0.0,
    fill: NoneValueType | Color | None = None,
    filter: NoneValueType | Filter | None = None,
    path_filter: NoneValueType | Filter | None = None,
    path_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    path_stroke_dashoffset: float | None = None,
    path_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    stroke: NoneValueType | Color | None = None,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    stroke_width: float | None = None,
    segments: tuple[
        Segment | BezierCurve | EllipticalArc
    ] = tuple(),
    source: LayoutElement | None = None,
    start_shorten: float = 0.0,
    target: LayoutElement | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_filter: NoneValueType | Filter | None = None,
    arrowhead_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    arrowhead_stroke_dashoffset: float | None = None,
    arrowhead_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None
)

Bases: SBGNSingleHeadedArc

Class for logic arc layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'e2a3ea9e-5bb2-4e42-a1ec-5579500346c8'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter	NoneValueType | Filter | None	The fill filter of the arc	None
path_fill	NoneValueType | Color | None		<momapy.drawing.NoneValueType object at 0x7f3954141040>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None		1.25
path_transform	NoneValueType | tuple[Transformation] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the arc	None
stroke_dashoffset	float | None	The stroke dashoffset of the arc	None
stroke_width	float | None	The stroke width of the arc	None
segments	tuple[Union[Segment, BezierCurve, EllipticalArc]]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None		1.25
arrowhead_transform	NoneValueType | tuple[Transformation] | None	The arrowhead transform of the arc	None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=elements,
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=actions,
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

LogicalOperator dataclass

LogicalOperator(
    *,
    id_: str = get_uuid4_as_str(),
    inputs: frozenset[LogicalOperatorInput] = frozenset()
)

Bases: SBGNModelElement

Class for logical operators

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'f6ba3aa7-571e-4e59-bbc7-cf9ee1b6d2d9'

LogicalOperatorInput dataclass

LogicalOperatorInput(
    *,
    id_: str = get_uuid4_as_str(),
    element: Union[
        EntityPool,
        ForwardRef(
            LogicalOperator, module=modules[__name__]
        ),
    ]
)

Bases: SBGNRole

Class for inputs of logical operators

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'082b147e-8ec6-4334-ae9b-901b010bf5ea'
element	EntityPool | ForwardRef('LogicalOperator', module=<module 'momapy.sbgn.pd' from '/home/rougny/code/momapy/src/momapy/sbgn/pd.py'>)		required

Macromolecule dataclass

Macromolecule(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None,
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset()
)

Bases: EntityPool

Class for macromolecules

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'0b38b799-698e-4fb6-8619-5351d845ff72'
compartment	Compartment | None		None
label	str | None		None

MacromoleculeLayout dataclass

MacromoleculeLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0,
    rounded_corners: float = 5.0
)

Bases: _SimpleMixin, SBGNNode

Class for macromolecule layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'6e8a04cc-a56e-4dab-a2cf-372ee5606533'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
rounded_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

MacromoleculeMultimer dataclass

MacromoleculeMultimer(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None,
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset(),
    subunits: frozenset[Subunit] = frozenset(),
    cardinality: int | None = None
)

Bases: Multimer

Class for macromolecule multimers

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'ca2aa06a-7f75-4ff0-b179-bad4a446e466'
compartment	Compartment | None		None
label	str | None		None
cardinality	int | None		None

MacromoleculeMultimerLayout dataclass

MacromoleculeMultimerLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    offset: float = 3.0,
    subunits_stroke: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_stroke_width: (
        tuple[NoneValueType | float] | None
    ) = None,
    subunits_stroke_dasharray: (
        tuple[NoneValueType | tuple[float]] | None
    ) = None,
    subunits_stroke_dashoffset: tuple[float] | None = None,
    subunits_fill: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_transform: (
        tuple[NoneValueType | tuple[Transformation]] | None
    ) = None,
    subunits_filter: (
        tuple[NoneValueType | Filter] | None
    ) = None,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0,
    rounded_corners: float = 5.0
)

Bases: _MultiMixin, SBGNNode

Class for macromolecule multimer layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'd8ec0c42-f1a6-48af-9a3f-d2a8e5cf8a93'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
offset	float		3.0
subunits_stroke	tuple[Union[NoneValueType, Color]] | None		None
subunits_stroke_width	tuple[Union[NoneValueType, float]] | None		None
subunits_stroke_dasharray	tuple[Union[NoneValueType, tuple[float]]] | None		None
subunits_stroke_dashoffset	tuple[float] | None		None
subunits_fill	tuple[Union[NoneValueType, Color]] | None		None
subunits_transform	tuple[Union[NoneValueType, tuple[Transformation]]] | None		None
subunits_filter	tuple[Union[NoneValueType, Filter]] | None		None
rounded_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

MacromoleculeMultimerSubunit dataclass

MacromoleculeMultimerSubunit(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset(),
    subunits: frozenset[Subunit] = frozenset(),
    cardinality: int | None = None
)

Bases: MultimerSubunit

Class for macromolecule multimer subunits

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'92b4fa77-e112-4cd3-9b14-fc36a4719003'
label	str | None		None
cardinality	int | None		None

MacromoleculeMultimerSubunitLayout dataclass

MacromoleculeMultimerSubunitLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    offset: float = 3.0,
    subunits_stroke: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_stroke_width: (
        tuple[NoneValueType | float] | None
    ) = None,
    subunits_stroke_dasharray: (
        tuple[NoneValueType | tuple[float]] | None
    ) = None,
    subunits_stroke_dashoffset: tuple[float] | None = None,
    subunits_fill: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_transform: (
        tuple[NoneValueType | tuple[Transformation]] | None
    ) = None,
    subunits_filter: (
        tuple[NoneValueType | Filter] | None
    ) = None,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0,
    rounded_corners: float = 5.0
)

Bases: _MultiMixin, SBGNNode

Class for macromolecule multimer subunit layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'5ffda5f0-6e3d-49b3-927c-a2aae8ec8140'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
offset	float		3.0
subunits_stroke	tuple[Union[NoneValueType, Color]] | None		None
subunits_stroke_width	tuple[Union[NoneValueType, float]] | None		None
subunits_stroke_dasharray	tuple[Union[NoneValueType, tuple[float]]] | None		None
subunits_stroke_dashoffset	tuple[float] | None		None
subunits_fill	tuple[Union[NoneValueType, Color]] | None		None
subunits_transform	tuple[Union[NoneValueType, tuple[Transformation]]] | None		None
subunits_filter	tuple[Union[NoneValueType, Filter]] | None		None
rounded_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

MacromoleculeSubunit dataclass

MacromoleculeSubunit(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset()
)

Bases: Subunit

Class for macromolecule subunits

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'20a95d74-9a38-4d82-b2aa-bfd58ac04508'
label	str | None		None

MacromoleculeSubunitLayout dataclass

MacromoleculeSubunitLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0,
    rounded_corners: float = 5.0
)

Bases: _SimpleMixin, SBGNNode

Class for macromolecule subunit layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'0f3b2b3a-6c5e-475e-b1aa-7f46dbb7bd78'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
rounded_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Modulation dataclass

Modulation(
    *,
    id_: str = get_uuid4_as_str(),
    source: EntityPool | LogicalOperator,
    target: Process
)

Bases: SBGNModelElement

Class for modulations

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'de0b96c9-5465-4610-9a90-6c468516ab3f'
source	EntityPool | LogicalOperator		required
target	Process		required

ModulationLayout dataclass

ModulationLayout(
    path_fill: NoneValueType | Color | None = NoneValue,
    path_stroke: NoneValueType | Color | None = black,
    path_stroke_width: float | None = 1.25,
    arrowhead_stroke: NoneValueType | Color | None = black,
    arrowhead_stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    end_shorten: float = 0.0,
    fill: NoneValueType | Color | None = None,
    filter: NoneValueType | Filter | None = None,
    path_filter: NoneValueType | Filter | None = None,
    path_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    path_stroke_dashoffset: float | None = None,
    path_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    stroke: NoneValueType | Color | None = None,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    stroke_width: float | None = None,
    segments: tuple[
        Segment | BezierCurve | EllipticalArc
    ] = tuple(),
    source: LayoutElement | None = None,
    start_shorten: float = 0.0,
    target: LayoutElement | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_fill: NoneValueType | Color | None = white,
    arrowhead_filter: NoneValueType | Filter | None = None,
    arrowhead_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    arrowhead_stroke_dashoffset: float | None = None,
    arrowhead_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_height: float = 10.0,
    arrowhead_width: float = 10.0
)

Bases: SBGNSingleHeadedArc

Class for modulation layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'75a6a148-d447-4142-85d6-073bbd9d0def'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter	NoneValueType | Filter | None	The fill filter of the arc	None
path_fill	NoneValueType | Color | None		<momapy.drawing.NoneValueType object at 0x7f3954141040>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None		1.25
path_transform	NoneValueType | tuple[Transformation] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the arc	None
stroke_dashoffset	float | None	The stroke dashoffset of the arc	None
stroke_width	float | None	The stroke width of the arc	None
segments	tuple[Union[Segment, BezierCurve, EllipticalArc]]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None		1.25
arrowhead_transform	NoneValueType | tuple[Transformation] | None	The arrowhead transform of the arc	None
arrowhead_height	float		10.0
arrowhead_width	float		10.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=elements,
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=actions,
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

Multimer dataclass

Multimer(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None,
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset(),
    subunits: frozenset[Subunit] = frozenset(),
    cardinality: int | None = None
)

Bases: Complex

Base class for multimers

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'0bd525e6-0b55-4b96-b548-b050e134dd90'
compartment	Compartment | None		None
label	str | None		None
cardinality	int | None		None

MultimerSubunit dataclass

MultimerSubunit(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset(),
    subunits: frozenset[Subunit] = frozenset(),
    cardinality: int | None = None
)

Bases: ComplexSubunit

Base class for multimer subunits

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'8fbd118f-98a0-4049-8bcd-18ae2313e662'
label	str | None		None
cardinality	int | None		None

NecessaryStimulation dataclass

NecessaryStimulation(
    *,
    id_: str = get_uuid4_as_str(),
    source: EntityPool | LogicalOperator,
    target: Process
)

Bases: Stimulation

Class for necessary stimulations

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'e3893a81-05ce-4e47-bbbf-bc4a46f94e73'
source	EntityPool | LogicalOperator		required
target	Process		required

NecessaryStimulationLayout dataclass

NecessaryStimulationLayout(
    path_fill: NoneValueType | Color | None = NoneValue,
    path_stroke: NoneValueType | Color | None = black,
    path_stroke_width: float | None = 1.25,
    arrowhead_fill: NoneValueType | Color | None = white,
    arrowhead_stroke: NoneValueType | Color | None = black,
    arrowhead_stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    end_shorten: float = 0.0,
    fill: NoneValueType | Color | None = None,
    filter: NoneValueType | Filter | None = None,
    path_filter: NoneValueType | Filter | None = None,
    path_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    path_stroke_dashoffset: float | None = None,
    path_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    stroke: NoneValueType | Color | None = None,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    stroke_width: float | None = None,
    segments: tuple[
        Segment | BezierCurve | EllipticalArc
    ] = tuple(),
    source: LayoutElement | None = None,
    start_shorten: float = 0.0,
    target: LayoutElement | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_filter: NoneValueType | Filter | None = None,
    arrowhead_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    arrowhead_stroke_dashoffset: float | None = None,
    arrowhead_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_bar_height: float = 12.0,
    arrowhead_sep: float = 3.0,
    arrowhead_triangle_height: float = 10.0,
    arrowhead_triangle_width: float = 10.0
)

Bases: SBGNSingleHeadedArc

Class for necessary stimulation layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'376c1d5b-054f-4214-9bc5-6da7106220db'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter	NoneValueType | Filter | None	The fill filter of the arc	None
path_fill	NoneValueType | Color | None		<momapy.drawing.NoneValueType object at 0x7f3954141040>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None		1.25
path_transform	NoneValueType | tuple[Transformation] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the arc	None
stroke_dashoffset	float | None	The stroke dashoffset of the arc	None
stroke_width	float | None	The stroke width of the arc	None
segments	tuple[Union[Segment, BezierCurve, EllipticalArc]]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None		1.25
arrowhead_transform	NoneValueType | tuple[Transformation] | None	The arrowhead transform of the arc	None
arrowhead_bar_height	float		12.0
arrowhead_sep	float		3.0
arrowhead_triangle_height	float		10.0
arrowhead_triangle_width	float		10.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=elements,
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=actions,
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

NotOperator dataclass

NotOperator(
    *,
    id_: str = get_uuid4_as_str(),
    inputs: frozenset[LogicalOperatorInput] = frozenset()
)

Bases: LogicalOperator

Class for not operators

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'1cdd6c6f-bdb1-4891-a29c-9a8a957f200a'

NotOperatorLayout dataclass

NotOperatorLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 30.0,
    direction: Direction = HORIZONTAL,
    left_to_right: bool = True,
    left_connector_length: float = 10.0,
    right_connector_length: float = 10.0,
    left_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    left_connector_stroke_width: float | None = None,
    left_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    left_connector_stroke_dashoffset: float | None = None,
    left_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    left_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    left_connector_filter: (
        NoneValueType | Filter | None
    ) = None,
    right_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    right_connector_stroke_width: float | None = None,
    right_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    right_connector_stroke_dashoffset: float | None = None,
    right_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    right_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    right_connector_filter: (
        NoneValueType | Filter | None
    ) = None
)

Bases: _ConnectorsMixin, _SimpleMixin, _TextMixin, SBGNNode

Class for not operator layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'756c38fe-ae12-4c18-b0a5-50c526d61690'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		30.0
direction	Direction		<Direction.HORIZONTAL: 1>
left_to_right	bool		True
left_connector_length	float		10.0
right_connector_length	float		10.0
left_connector_stroke	NoneValueType | Color | None		None
left_connector_stroke_width	float | None		None
left_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
left_connector_stroke_dashoffset	float | None		None
left_connector_fill	NoneValueType | Color | None		None
left_connector_transform	NoneValueType | tuple[Transformation] | None		None
left_connector_filter	NoneValueType | Filter | None		None
right_connector_stroke	NoneValueType | Color | None		None
right_connector_stroke_width	float | None		None
right_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
right_connector_stroke_dashoffset	float | None		None
right_connector_fill	NoneValueType | Color | None		None
right_connector_transform	NoneValueType | tuple[Transformation] | None		None
right_connector_filter	NoneValueType | Filter | None		None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

NucleicAcidFeature dataclass

NucleicAcidFeature(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None,
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset()
)

Bases: EntityPool

Class for nucleic acid features

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'8066843a-00c9-4087-a5b4-661402c50eea'
compartment	Compartment | None		None
label	str | None		None

NucleicAcidFeatureLayout dataclass

NucleicAcidFeatureLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0,
    rounded_corners: float = 5.0
)

Bases: _SimpleMixin, SBGNNode

Class for nucleic acid feature layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'9aafad97-027b-4eee-b65c-5b2d3e2cbc58'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
rounded_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

NucleicAcidFeatureMultimer dataclass

NucleicAcidFeatureMultimer(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None,
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset(),
    subunits: frozenset[Subunit] = frozenset(),
    cardinality: int | None = None
)

Bases: Multimer

Class for nucleic acid feature multimers

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'72a78b2d-7b21-4288-a7b0-f83720bc2ca3'
compartment	Compartment | None		None
label	str | None		None
cardinality	int | None		None

NucleicAcidFeatureMultimerLayout dataclass

NucleicAcidFeatureMultimerLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    offset: float = 3.0,
    subunits_stroke: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_stroke_width: (
        tuple[NoneValueType | float] | None
    ) = None,
    subunits_stroke_dasharray: (
        tuple[NoneValueType | tuple[float]] | None
    ) = None,
    subunits_stroke_dashoffset: tuple[float] | None = None,
    subunits_fill: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_transform: (
        tuple[NoneValueType | tuple[Transformation]] | None
    ) = None,
    subunits_filter: (
        tuple[NoneValueType | Filter] | None
    ) = None,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0,
    rounded_corners: float = 5.0
)

Bases: _MultiMixin, SBGNNode

Class for nucleic acid feature multimer layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'aec4d54c-4eda-4b94-af9a-53444b2b814b'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
offset	float		3.0
subunits_stroke	tuple[Union[NoneValueType, Color]] | None		None
subunits_stroke_width	tuple[Union[NoneValueType, float]] | None		None
subunits_stroke_dasharray	tuple[Union[NoneValueType, tuple[float]]] | None		None
subunits_stroke_dashoffset	tuple[float] | None		None
subunits_fill	tuple[Union[NoneValueType, Color]] | None		None
subunits_transform	tuple[Union[NoneValueType, tuple[Transformation]]] | None		None
subunits_filter	tuple[Union[NoneValueType, Filter]] | None		None
rounded_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

NucleicAcidFeatureMultimerSubunit dataclass

NucleicAcidFeatureMultimerSubunit(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset(),
    subunits: frozenset[Subunit] = frozenset(),
    cardinality: int | None = None
)

Bases: MultimerSubunit

Class for nucleic acid feature multimer subunits

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'bef40879-44a3-4638-a904-053011f3ae0e'
label	str | None		None
cardinality	int | None		None

NucleicAcidFeatureMultimerSubunitLayout dataclass

NucleicAcidFeatureMultimerSubunitLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    offset: float = 3.0,
    subunits_stroke: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_stroke_width: (
        tuple[NoneValueType | float] | None
    ) = None,
    subunits_stroke_dasharray: (
        tuple[NoneValueType | tuple[float]] | None
    ) = None,
    subunits_stroke_dashoffset: tuple[float] | None = None,
    subunits_fill: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_transform: (
        tuple[NoneValueType | tuple[Transformation]] | None
    ) = None,
    subunits_filter: (
        tuple[NoneValueType | Filter] | None
    ) = None,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0,
    rounded_corners: float = 5.0
)

Bases: _MultiMixin, SBGNNode

Class for nucleic acid feature multimer subunit layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'6b4a1dc8-4d8d-468f-8814-7cacf7429b25'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
offset	float		3.0
subunits_stroke	tuple[Union[NoneValueType, Color]] | None		None
subunits_stroke_width	tuple[Union[NoneValueType, float]] | None		None
subunits_stroke_dasharray	tuple[Union[NoneValueType, tuple[float]]] | None		None
subunits_stroke_dashoffset	tuple[float] | None		None
subunits_fill	tuple[Union[NoneValueType, Color]] | None		None
subunits_transform	tuple[Union[NoneValueType, tuple[Transformation]]] | None		None
subunits_filter	tuple[Union[NoneValueType, Filter]] | None		None
rounded_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

NucleicAcidFeatureSubunit dataclass

NucleicAcidFeatureSubunit(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset()
)

Bases: Subunit

Class for nucleic acid feature subunits

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'66fecbc8-7657-4c51-b62c-e93164f6b0ea'
label	str | None		None

NucleicAcidFeatureSubunitLayout dataclass

NucleicAcidFeatureSubunitLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0,
    rounded_corners: float = 5.0
)

Bases: _SimpleMixin, SBGNNode

Class for nucleic acid feature subunit layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'56f4cf8a-8d4d-4bba-b5b7-45fc0d25ced3'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
rounded_corners	float		5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

OmittedProcess dataclass

OmittedProcess(
    *,
    id_: str = get_uuid4_as_str(),
    reactants: frozenset[Reactant] = frozenset(),
    products: frozenset[Product] = frozenset(),
    reversible: bool = False
)

Bases: GenericProcess

Class for omitted processes

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'e087ed07-f724-47e5-ac99-c9be091006cf'
reversible	bool		False

OmittedProcessLayout dataclass

OmittedProcessLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 20.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 20.0,
    direction: Direction = HORIZONTAL,
    left_to_right: bool = True,
    left_connector_length: float = 10.0,
    right_connector_length: float = 10.0,
    left_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    left_connector_stroke_width: float | None = None,
    left_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    left_connector_stroke_dashoffset: float | None = None,
    left_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    left_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    left_connector_filter: (
        NoneValueType | Filter | None
    ) = None,
    right_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    right_connector_stroke_width: float | None = None,
    right_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    right_connector_stroke_dashoffset: float | None = None,
    right_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    right_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    right_connector_filter: (
        NoneValueType | Filter | None
    ) = None
)

Bases: _ConnectorsMixin, _SimpleMixin, _TextMixin, SBGNNode

Class for omitted process layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'dc2bd99b-1fcf-4f90-9a2c-923b624edf49'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		20.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		20.0
direction	Direction		<Direction.HORIZONTAL: 1>
left_to_right	bool		True
left_connector_length	float		10.0
right_connector_length	float		10.0
left_connector_stroke	NoneValueType | Color | None		None
left_connector_stroke_width	float | None		None
left_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
left_connector_stroke_dashoffset	float | None		None
left_connector_fill	NoneValueType | Color | None		None
left_connector_transform	NoneValueType | tuple[Transformation] | None		None
left_connector_filter	NoneValueType | Filter | None		None
right_connector_stroke	NoneValueType | Color | None		None
right_connector_stroke_width	float | None		None
right_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
right_connector_stroke_dashoffset	float | None		None
right_connector_fill	NoneValueType | Color | None		None
right_connector_transform	NoneValueType | tuple[Transformation] | None		None
right_connector_filter	NoneValueType | Filter | None		None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

OrOperator dataclass

OrOperator(
    *,
    id_: str = get_uuid4_as_str(),
    inputs: frozenset[LogicalOperatorInput] = frozenset()
)

Bases: LogicalOperator

Class for or operators

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'bcf3e502-739d-4bbb-b1fd-4d06bb268d60'

OrOperatorLayout dataclass

OrOperatorLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 30.0,
    direction: Direction = HORIZONTAL,
    left_to_right: bool = True,
    left_connector_length: float = 10.0,
    right_connector_length: float = 10.0,
    left_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    left_connector_stroke_width: float | None = None,
    left_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    left_connector_stroke_dashoffset: float | None = None,
    left_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    left_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    left_connector_filter: (
        NoneValueType | Filter | None
    ) = None,
    right_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    right_connector_stroke_width: float | None = None,
    right_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    right_connector_stroke_dashoffset: float | None = None,
    right_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    right_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    right_connector_filter: (
        NoneValueType | Filter | None
    ) = None
)

Bases: _ConnectorsMixin, _SimpleMixin, _TextMixin, SBGNNode

Class for or operator layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'dcb8b9f2-4fea-4068-9325-a33e94d3e241'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		30.0
direction	Direction		<Direction.HORIZONTAL: 1>
left_to_right	bool		True
left_connector_length	float		10.0
right_connector_length	float		10.0
left_connector_stroke	NoneValueType | Color | None		None
left_connector_stroke_width	float | None		None
left_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
left_connector_stroke_dashoffset	float | None		None
left_connector_fill	NoneValueType | Color | None		None
left_connector_transform	NoneValueType | tuple[Transformation] | None		None
left_connector_filter	NoneValueType | Filter | None		None
right_connector_stroke	NoneValueType | Color | None		None
right_connector_stroke_width	float | None		None
right_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
right_connector_stroke_dashoffset	float | None		None
right_connector_fill	NoneValueType | Color | None		None
right_connector_transform	NoneValueType | tuple[Transformation] | None		None
right_connector_filter	NoneValueType | Filter | None		None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

PerturbingAgent dataclass

PerturbingAgent(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None,
    label: str | None = None
)

Bases: EntityPool

Class for perturbing agents

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'eaeb3960-d221-41e3-908f-c5bc2888b7a4'
compartment	Compartment | None		None
label	str | None		None

PerturbingAgentLayout dataclass

PerturbingAgentLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0,
    angle: float = 70.0
)

Bases: _SimpleMixin, SBGNNode

Class for perturbing agent layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'b118e33c-b917-4d3a-97dc-f486f934e23c'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
angle	float		70.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
angle	float	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = 70.0

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Phenotype dataclass

Phenotype(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None
)

Bases: Process

Class for phenotypes

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'dca09d63-b0ae-43ad-a578-37bd9b1ec16b'
label	str | None		None

PhenotypeLayout dataclass

PhenotypeLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0,
    angle: float = 70.0
)

Bases: _SimpleMixin, SBGNNode

Class for phenotype layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'bd5c356a-45bc-4da4-8a49-986bbec578fc'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
angle	float		70.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
angle	float	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = 70.0

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Process dataclass

Process(*, id_: str = get_uuid4_as_str())

Bases: SBGNModelElement

Base class for processes

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'ca548e0a-ef94-465d-81ae-2350fbd2cd94'

Product dataclass

Product(
    *,
    id_: str = get_uuid4_as_str(),
    element: EntityPool,
    stoichiometry: int | None = None
)

Bases: FluxRole

Class for products

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'73a396f9-339c-4f72-909b-5cf49145aa2c'
element	EntityPool		required
stoichiometry	int | None		None

ProductionLayout dataclass

ProductionLayout(
    path_fill: NoneValueType | Color | None = NoneValue,
    path_stroke: NoneValueType | Color | None = black,
    path_stroke_width: float | None = 1.25,
    arrowhead_stroke: NoneValueType | Color | None = black,
    arrowhead_stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    end_shorten: float = 0.0,
    fill: NoneValueType | Color | None = None,
    filter: NoneValueType | Filter | None = None,
    path_filter: NoneValueType | Filter | None = None,
    path_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    path_stroke_dashoffset: float | None = None,
    path_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    stroke: NoneValueType | Color | None = None,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    stroke_width: float | None = None,
    segments: tuple[
        Segment | BezierCurve | EllipticalArc
    ] = tuple(),
    source: LayoutElement | None = None,
    start_shorten: float = 0.0,
    target: LayoutElement | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_fill: NoneValueType | Color | None = black,
    arrowhead_filter: NoneValueType | Filter | None = None,
    arrowhead_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    arrowhead_stroke_dashoffset: float | None = None,
    arrowhead_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_height: float = 10.0,
    arrowhead_width: float = 10.0
)

Bases: SBGNSingleHeadedArc

Class for production layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'6e4ae224-7ab6-454d-b0f1-037e0c369bc8'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter	NoneValueType | Filter | None	The fill filter of the arc	None
path_fill	NoneValueType | Color | None		<momapy.drawing.NoneValueType object at 0x7f3954141040>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None		1.25
path_transform	NoneValueType | tuple[Transformation] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the arc	None
stroke_dashoffset	float | None	The stroke dashoffset of the arc	None
stroke_width	float | None	The stroke width of the arc	None
segments	tuple[Union[Segment, BezierCurve, EllipticalArc]]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None		1.25
arrowhead_transform	NoneValueType | tuple[Transformation] | None	The arrowhead transform of the arc	None
arrowhead_height	float		10.0
arrowhead_width	float		10.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=elements,
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=actions,
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

Reactant dataclass

Reactant(
    *,
    id_: str = get_uuid4_as_str(),
    element: EntityPool,
    stoichiometry: int | None = None
)

Bases: FluxRole

Class for reactants

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'2c6ed4ec-06f9-4ca7-8695-40c5544785ae'
element	EntityPool		required
stoichiometry	int | None		None

SBGNPDLayout dataclass

SBGNPDLayout(
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    fill: NoneValueType | Color | None = white,
    filter: NoneValueType | Filter | None = None,
    height: float,
    label: TextLayout | None = None,
    position: Point,
    stroke: NoneValueType | Color | None = None,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    stroke_width: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = None
)

Bases: SBGNLayout

Class for SBGN-PD layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'dd7f5ba3-a382-46cc-b8a0-5238f91d63e9'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	required
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	None
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	None
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float	The stroke width of the node	None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
is_sublayout	Return true if another given layout is a sublayout of the layout, false otherwise
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

is_sublayout

is_sublayout(other, flattened=False, unordered=False)

Return true if another given layout is a sublayout of the layout, false otherwise

Source code in src/momapy/core.py

def is_sublayout(self, other, flattened=False, unordered=False):
    """Return `true` if another given layout is a sublayout of the layout, `false` otherwise"""

    def _is_sublist(list1, list2, unordered=False) -> bool:
        if not unordered:
            i = 0
            for elem1 in list1:
                elem2 = list2[i]
                while elem2 != elem1 and i < len(list2) - 1:
                    i += 1
                    elem2 = list2[i]
                if not elem2 == elem1:
                    return False
                i += 1
        else:
            dlist1 = collections.defaultdict(int)
            dlist2 = collections.defaultdict(int)
            for elem1 in list1:
                dlist1[elem1] += 1
            for elem2 in list2:
                dlist2[elem2] += 1
            for elem in dlist1:
                if dlist1[elem] > dlist2[elem]:
                    return False
        return True

    if self.childless() != other.childless():
        return False
    if flattened:
        return _is_sublist(
            self.flattened()[1:],
            other.flattened()[1:],
            unordered=unordered,
        )
    return _is_sublist(
        self.children(), other.children(), unordered=unordered
    )

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

SBGNPDLayoutBuilder module-attribute

SBGNPDLayoutBuilder = get_or_make_builder_cls(SBGNPDLayout)

Class for SBGN-PD layout builders

SBGNPDMap dataclass

SBGNPDMap(
    *,
    id_: str = get_uuid4_as_str(),
    model: SBGNPDModel,
    layout: SBGNPDLayout,
    layout_model_mapping: LayoutModelMapping | None = None
)

Bases: SBGNMap

Class for SBGN-PD maps

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'6daf3565-a3f7-4d28-97e4-7f4308f3c069'
model	SBGNPDModel		None
layout	SBGNPDLayout		None
layout_model_mapping	LayoutModelMapping | None	The layout model mapping of the map	None

Methods:

Name	Description
get_mapping	Return the layout elements mapped to the given model element
is_submap	Return true if another given map is a submap of the Map, false otherwise

get_mapping

get_mapping(
    key: (
        ModelElement | _MappingElementType | _MappingKeyType
    ),
    expand: bool = True,
    unpack: bool = False,
)

Return the layout elements mapped to the given model element

Source code in src/momapy/core.py

def get_mapping(
    self,
    key: ModelElement | _MappingElementType | _MappingKeyType,
    expand: bool = True,
    unpack: bool = False,
):
    """Return the layout elements mapped to the given model element"""
    return self.layout_model_mapping.get_mapping(
        key=key, expand=expand, unpack=unpack
    )

is_submap

is_submap(other)

Return true if another given map is a submap of the Map, false otherwise

Source code in src/momapy/core.py

def is_submap(self, other):
    """Return `true` if another given map is a submap of the `Map`, `false` otherwise"""
    return (
        self.model.is_submodel(other.model)
        and self.layout.is_sublayout(other.layout)
        and self.layout_model_mapping.is_submapping(
            other.layout_model_mapping
        )
    )

SBGNPDMapBuilder module-attribute

SBGNPDMapBuilder = get_or_make_builder_cls(
    SBGNPDMap,
    builder_namespace={
        "new_model": _sbgnpd_map_builder_new_model,
        "new_layout": _sbgnpd_map_builder_new_layout,
    },
)

Class for SBGN-PD map builders

SBGNPDModel dataclass

SBGNPDModel(
    *,
    id_: str = get_uuid4_as_str(),
    entity_pools: frozenset[EntityPool] = frozenset(),
    processes: frozenset[Process] = frozenset(),
    compartments: frozenset[Compartment] = frozenset(),
    modulations: frozenset[Modulation] = frozenset(),
    logical_operators: frozenset[
        LogicalOperator
    ] = frozenset(),
    equivalence_operators: frozenset[
        EquivalenceOperator
    ] = frozenset(),
    submaps: frozenset[Submap] = frozenset(),
    tags: frozenset[Tag] = frozenset()
)

Bases: SBGNModel

Class for SBGN-PD models

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'324fe142-8cb0-4186-a2c2-38465c9926c6'

Methods:

Name	Description
is_ovav	Return true if the SBGN-PD model respects the Once a Variable Always a Variable (OVAV) rule, false otherwise
is_submodel	Return true if another given SBGN-PD model is a submodel of the SBGN-PD model, false otherwise

is_ovav

is_ovav() -> bool

Return true if the SBGN-PD model respects the Once a Variable Always a Variable (OVAV) rule, false otherwise

Source code in src/momapy/sbgn/pd.py

def is_ovav(self) -> bool:
    """Return `true` if the SBGN-PD model respects the Once a Variable Always a Variable (OVAV) rule, `false` otherwise"""
    subunit_cls_entity_pool_cls_mapping = {
        MacromoleculeSubunit: Macromolecule,
        NucleicAcidFeatureSubunit: NucleicAcidFeature,
        ComplexSubunit: Complex,
        SimpleChemicalSubunit: SimpleChemical,
        MacromoleculeMultimerSubunit: MacromoleculeMultimer,
        NucleicAcidFeatureMultimerSubunit: NucleicAcidFeatureMultimer,
        ComplexMultimerSubunit: ComplexMultimer,
        SimpleChemicalMultimerSubunit: SimpleChemicalMultimer,
    }

    def _check_entities(entities, entity_variables_mapping=None):
        if entity_variables_mapping is None:
            entity_variables_mapping = {}
        for entity in entities:
            if hasattr(entity, "state_variables"):
                variables = set(
                    [sv.variable for sv in entity.state_variables]
                )
                attributes = []
                for field in dataclasses.fields(entity):
                    if field.name != "state_variables":
                        attributes.append(field.name)
                args = {attr: getattr(entity, attr) for attr in attributes}
                if isinstance(entity, Subunit):
                    cls = subunit_cls_entity_pool_cls_mapping[type(entity)]
                else:
                    cls = type(entity)
                entity_no_svs = cls(**args)
                if entity_no_svs not in entity_variables_mapping:
                    entity_variables_mapping[entity_no_svs] = variables
                else:
                    if (
                        entity_variables_mapping[entity_no_svs]
                        != variables
                    ):
                        return False
            if hasattr(entity, "subunits"):
                is_ovav = _check_entities(
                    entity.subunits, entity_variables_mapping
                )
                if not is_ovav:
                    return False
        return True

    return _check_entities(self.entity_pools)

is_submodel

is_submodel(other)

Return true if another given SBGN-PD model is a submodel of the SBGN-PD model, false otherwise

Source code in src/momapy/sbgn/pd.py

def is_submodel(self, other):
    """Return `true` if another given SBGN-PD model is a submodel of the SBGN-PD model, `false` otherwise"""
    return (
        self.entity_pools.issubset(other.entity_pools)
        and self.processes.issubset(other.processes)
        and self.compartments.issubset(other.compartments)
        and self.modulations.issubset(other.modulations)
        and self.logical_operators.issubset(other.logical_operators)
        and self.equivalence_operators.issubset(
            other.equivalence_operators
        )
        and self.submaps.issubset(other.submaps)
        and self.tags.issubset(other.tags)
    )

SBGNPDModelBuilder module-attribute

SBGNPDModelBuilder = get_or_make_builder_cls(SBGNPDModel)

Class for SBGN-PD model builders

SimpleChemical dataclass

SimpleChemical(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None,
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset()
)

Bases: EntityPool

Class for simple chemical

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'dc37d284-6600-4ca9-930d-55dac4de01e4'
compartment	Compartment | None		None
label	str | None		None

SimpleChemicalLayout dataclass

SimpleChemicalLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 30.0
)

Bases: _SimpleMixin, SBGNNode

Class for simple chemical layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'3e281415-3d9c-4b5c-b2e3-11b577e4177f'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		30.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

SimpleChemicalMultimer dataclass

SimpleChemicalMultimer(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None,
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset(),
    subunits: frozenset[Subunit] = frozenset(),
    cardinality: int | None = None
)

Bases: Multimer

Class for simple chemical multimers

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'ce3f4568-f6c3-4de7-8945-e375dd149da9'
compartment	Compartment | None		None
label	str | None		None
cardinality	int | None		None

SimpleChemicalMultimerLayout dataclass

SimpleChemicalMultimerLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    offset: float = 3.0,
    subunits_stroke: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_stroke_width: (
        tuple[NoneValueType | float] | None
    ) = None,
    subunits_stroke_dasharray: (
        tuple[NoneValueType | tuple[float]] | None
    ) = None,
    subunits_stroke_dashoffset: tuple[float] | None = None,
    subunits_fill: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_transform: (
        tuple[NoneValueType | tuple[Transformation]] | None
    ) = None,
    subunits_filter: (
        tuple[NoneValueType | Filter] | None
    ) = None,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 30.0
)

Bases: _MultiMixin, SBGNNode

Class for simple chemical multimer layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'03e5361e-ac83-4fb8-a936-89505055bbff'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		30.0
offset	float		3.0
subunits_stroke	tuple[Union[NoneValueType, Color]] | None		None
subunits_stroke_width	tuple[Union[NoneValueType, float]] | None		None
subunits_stroke_dasharray	tuple[Union[NoneValueType, tuple[float]]] | None		None
subunits_stroke_dashoffset	tuple[float] | None		None
subunits_fill	tuple[Union[NoneValueType, Color]] | None		None
subunits_transform	tuple[Union[NoneValueType, tuple[Transformation]]] | None		None
subunits_filter	tuple[Union[NoneValueType, Filter]] | None		None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

SimpleChemicalMultimerSubunit dataclass

SimpleChemicalMultimerSubunit(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset(),
    subunits: frozenset[Subunit] = frozenset(),
    cardinality: int | None = None
)

Bases: MultimerSubunit

Class for simple chemical multimer subunits

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'8a8e241d-aeae-4865-bace-9c2e4342ad8c'
label	str | None		None
cardinality	int | None		None

SimpleChemicalMultimerSubunitLayout dataclass

SimpleChemicalMultimerSubunitLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    offset: float = 3.0,
    subunits_stroke: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_stroke_width: (
        tuple[NoneValueType | float] | None
    ) = None,
    subunits_stroke_dasharray: (
        tuple[NoneValueType | tuple[float]] | None
    ) = None,
    subunits_stroke_dashoffset: tuple[float] | None = None,
    subunits_fill: (
        tuple[NoneValueType | Color] | None
    ) = None,
    subunits_transform: (
        tuple[NoneValueType | tuple[Transformation]] | None
    ) = None,
    subunits_filter: (
        tuple[NoneValueType | Filter] | None
    ) = None,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0
)

Bases: _MultiMixin, SBGNNode

Class for simple chemical multimer subunit layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'21e212cf-5505-4d2f-a3f4-51b3ef25c2e6'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0
offset	float		3.0
subunits_stroke	tuple[Union[NoneValueType, Color]] | None		None
subunits_stroke_width	tuple[Union[NoneValueType, float]] | None		None
subunits_stroke_dasharray	tuple[Union[NoneValueType, tuple[float]]] | None		None
subunits_stroke_dashoffset	tuple[float] | None		None
subunits_fill	tuple[Union[NoneValueType, Color]] | None		None
subunits_transform	tuple[Union[NoneValueType, tuple[Transformation]]] | None		None
subunits_filter	tuple[Union[NoneValueType, Filter]] | None		None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

SimpleChemicalSubunit dataclass

SimpleChemicalSubunit(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    state_variables: frozenset[StateVariable] = frozenset(),
    units_of_information: frozenset[
        UnitOfInformation
    ] = frozenset()
)

Bases: Subunit

Class for simple chemical subunits

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'f1c510a9-2a57-4c96-b562-fe7a286efb87'
label	str | None		None

SimpleChemicalSubunitLayout dataclass

SimpleChemicalSubunitLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 30.0
)

Bases: _SimpleMixin, SBGNNode

Class for simple chemical subunit layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'291b4cb6-c41e-4d58-950a-980d80128455'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		30.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

StateVariable dataclass

StateVariable(
    *,
    id_: str = get_uuid4_as_str(),
    variable: str | None = None,
    value: str | None = None,
    order: int | None = None
)

Bases: SBGNAuxiliaryUnit

Class for state variables

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'632b5ec6-3617-4bff-b042-832bb3a2fe21'
variable	str | None		None
value	str | None		None
order	int | None		None

StateVariableLayout dataclass

StateVariableLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 12.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 12.0
)

Bases: _SimpleMixin, SBGNNode

Class for state variable layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'75c7a0d2-6ade-4b34-bc3e-1721c0c5ffd1'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		12.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		12.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Stimulation dataclass

Stimulation(
    *,
    id_: str = get_uuid4_as_str(),
    source: EntityPool | LogicalOperator,
    target: Process
)

Bases: Modulation

Class for stimulations

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'06355440-f229-43db-bd90-7f06f597ea9a'
source	EntityPool | LogicalOperator		required
target	Process		required

StimulationLayout dataclass

StimulationLayout(
    path_fill: NoneValueType | Color | None = NoneValue,
    path_stroke: NoneValueType | Color | None = black,
    path_stroke_width: float | None = 1.25,
    arrowhead_fill: NoneValueType | Color | None = white,
    arrowhead_stroke: NoneValueType | Color | None = black,
    arrowhead_stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    end_shorten: float = 0.0,
    fill: NoneValueType | Color | None = None,
    filter: NoneValueType | Filter | None = None,
    path_filter: NoneValueType | Filter | None = None,
    path_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    path_stroke_dashoffset: float | None = None,
    path_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    stroke: NoneValueType | Color | None = None,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    stroke_width: float | None = None,
    segments: tuple[
        Segment | BezierCurve | EllipticalArc
    ] = tuple(),
    source: LayoutElement | None = None,
    start_shorten: float = 0.0,
    target: LayoutElement | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_filter: NoneValueType | Filter | None = None,
    arrowhead_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    arrowhead_stroke_dashoffset: float | None = None,
    arrowhead_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    arrowhead_height: float = 10.0,
    arrowhead_width: float = 10.0
)

Bases: SBGNSingleHeadedArc

Class for stimulation layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'b9dce6e4-1bde-4ab6-928d-29b9fbcebab6'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter	NoneValueType | Filter | None	The fill filter of the arc	None
path_fill	NoneValueType | Color | None		<momapy.drawing.NoneValueType object at 0x7f3954141040>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None		1.25
path_transform	NoneValueType | tuple[Transformation] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the arc	None
stroke_dashoffset	float | None	The stroke dashoffset of the arc	None
stroke_width	float | None	The stroke width of the arc	None
segments	tuple[Union[Segment, BezierCurve, EllipticalArc]]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None		1.25
arrowhead_transform	NoneValueType | tuple[Transformation] | None	The arrowhead transform of the arc	None
arrowhead_height	float		10.0
arrowhead_width	float		10.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead
arrowhead_length	Return the length of the single-headed arc arrowhead
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc
bbox	Compute and return the bounding box of the layout element
childless	Return a copy of the arc with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
fraction	Return the position and angle on the arc at a given fraction (of the total arc length)
length	Return the total length of the arc path
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_base(self) -> momapy.geometry.Point:
    """Return the arrowhead base anchor point of the single-headed arc"""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """

    point = momapy.drawing.get_drawing_elements_border(
        self.arrowhead_drawing_elements(), point
    )
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=elements,
        fill=self.arrowhead_fill,
        filter=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead

Source code in src/momapy/core.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc

Source code in src/momapy/core.py

def arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the arrowhead tip anchor point of the single-headed arc"""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

childless

childless() -> Self

Return a copy of the arc with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the arc with no children"""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc

Source code in src/momapy/core.py

def end_point(self) -> momapy.geometry.Point:
    """Return the ending point of the arc"""
    return self.points()[-1]

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length)

Source code in src/momapy/core.py

def fraction(self, fraction: float) -> tuple[momapy.geometry.Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length)"""
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

def length(self):
    """Return the total length of the arc path"""
    return sum([segment.length() for segment in self.segments])

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.py

def path_drawing_elements(self) -> list[momapy.drawing.Path]:
    """Return the drawing elements of the single-headed arc path"""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            momapy.drawing.MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(
            self.start_shorten, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            momapy.drawing.MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = momapy.drawing.Path(
        actions=actions,
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path

Source code in src/momapy/core.py

def points(self) -> list[momapy.geometry.Point]:
    """Return the points of the arc path"""
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the arc"""
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

StoichiometricProcess dataclass

StoichiometricProcess(
    *,
    id_: str = get_uuid4_as_str(),
    reactants: frozenset[Reactant] = frozenset(),
    products: frozenset[Product] = frozenset(),
    reversible: bool = False
)

Bases: Process

Base class for stoichiometric processes

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'b051d98f-fade-479c-b6c5-507e0671c70f'
reversible	bool		False

Submap dataclass

Submap(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    terminals: frozenset[Terminal] = frozenset()
)

Bases: SBGNModelElement

Class for submaps

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'512ced33-e625-4507-8916-cb05ef6f7558'
label	str | None		None

SubmapLayout dataclass

SubmapLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 80.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    stroke_width: float = 2.25,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 80.0
)

Bases: _SimpleMixin, SBGNNode

Class for submap layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'150350f5-766e-477d-9edc-d87809e45098'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		80.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float		2.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		80.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

Subunit dataclass

Subunit(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None
)

Bases: SBGNAuxiliaryUnit

Base class for subunits

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'e1b51bf3-36f8-4c01-9acc-140a74d0f58b'
label	str | None		None

Tag dataclass

Tag(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    reference: TagReference | None = None
)

Bases: SBGNModelElement

Class for tags

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'6565fa6f-d2bb-4259-a0eb-17092dbf6974'
label	str | None		None
reference	TagReference | None		None

TagLayout dataclass

TagLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 35.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 35.0,
    direction: Direction = RIGHT,
    angle: float = 70.0
)

Bases: _SimpleMixin, SBGNNode

Class for tag layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'8cf899be-4a63-447d-9693-98993f67e034'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		35.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		35.0
direction	Direction		<Direction.RIGHT: 4>
angle	float		70.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
angle	float	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = 70.0

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

TagReference dataclass

TagReference(
    *,
    id_: str = get_uuid4_as_str(),
    element: EntityPool | Compartment
)

Bases: SBGNRole

Class for tag references

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'ad3901a3-d865-4474-ad68-9ce61c950c91'
element	EntityPool | Compartment		required

Terminal dataclass

Terminal(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None,
    reference: TerminalReference | None = None
)

Bases: SBGNAuxiliaryUnit

Class for terminals

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'a7c7d16f-5de3-41f0-ae8d-288badaf08fa'
label	str | None		None
reference	TerminalReference | None		None

TerminalLayout dataclass

TerminalLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 35.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 35.0,
    direction: Direction = RIGHT,
    angle: float = 70.0
)

Bases: _SimpleMixin, SBGNNode

Class for terminal layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'3577cca9-036b-4791-8b00-572785efdda6'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		35.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		35.0
direction	Direction		<Direction.RIGHT: 4>
angle	float		70.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
angle	float	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = 70.0

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

TerminalReference dataclass

TerminalReference(
    *,
    id_: str = get_uuid4_as_str(),
    element: EntityPool | Compartment
)

Bases: SBGNRole

Class for terminal references

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'ec3bf6c6-9333-474b-b6b9-e5d1ca8c08dd'
element	EntityPool | Compartment		required

UncertainProcess dataclass

UncertainProcess(
    *,
    id_: str = get_uuid4_as_str(),
    reactants: frozenset[Reactant] = frozenset(),
    products: frozenset[Product] = frozenset(),
    reversible: bool = False
)

Bases: StoichiometricProcess

Class for uncertain processes

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'e32eb439-370f-4d23-a675-3707342480df'
reversible	bool		False

UncertainProcessLayout dataclass

UncertainProcessLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 20.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 20.0,
    direction: Direction = HORIZONTAL,
    left_to_right: bool = True,
    left_connector_length: float = 10.0,
    right_connector_length: float = 10.0,
    left_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    left_connector_stroke_width: float | None = None,
    left_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    left_connector_stroke_dashoffset: float | None = None,
    left_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    left_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    left_connector_filter: (
        NoneValueType | Filter | None
    ) = None,
    right_connector_stroke: (
        NoneValueType | Color | None
    ) = None,
    right_connector_stroke_width: float | None = None,
    right_connector_stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    right_connector_stroke_dashoffset: float | None = None,
    right_connector_fill: (
        NoneValueType | Color | None
    ) = None,
    right_connector_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    right_connector_filter: (
        NoneValueType | Filter | None
    ) = None
)

Bases: _ConnectorsMixin, _SimpleMixin, _TextMixin, SBGNNode

Class for uncertain process layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'c8090a9e-3a93-44f6-963e-3a826bdef772'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		20.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		20.0
direction	Direction		<Direction.HORIZONTAL: 1>
left_to_right	bool		True
left_connector_length	float		10.0
right_connector_length	float		10.0
left_connector_stroke	NoneValueType | Color | None		None
left_connector_stroke_width	float | None		None
left_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
left_connector_stroke_dashoffset	float | None		None
left_connector_fill	NoneValueType | Color | None		None
left_connector_transform	NoneValueType | tuple[Transformation] | None		None
left_connector_filter	NoneValueType | Filter | None		None
right_connector_stroke	NoneValueType | Color | None		None
right_connector_stroke_width	float | None		None
right_connector_stroke_dasharray	NoneValueType | tuple[float] | None		None
right_connector_stroke_dashoffset	float | None		None
right_connector_fill	NoneValueType | Color | None		None
right_connector_transform	NoneValueType | tuple[Transformation] | None		None
right_connector_filter	NoneValueType | Filter | None		None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

UnitOfInformation dataclass

UnitOfInformation(
    *,
    id_: str = get_uuid4_as_str(),
    value: str,
    prefix: str | None = None
)

Bases: SBGNAuxiliaryUnit

Class for units of information

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'0cef4ab4-be0c-4244-a601-84a89dac311c'
value	str		required
prefix	str | None		None

UnitOfInformationLayout dataclass

UnitOfInformationLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 12.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 12.0
)

Bases: _SimpleMixin, SBGNNode

Class for unit of information layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'6318b7d1-7886-41a7-8607-f4dd0f115201'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		12.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		12.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

UnspecifiedEntity dataclass

UnspecifiedEntity(
    *,
    id_: str = get_uuid4_as_str(),
    compartment: Compartment | None = None,
    label: str | None = None
)

Bases: EntityPool

Class for unspecified entities

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'9372975d-a7fb-4862-a3ac-1702fe1e7728'
compartment	Compartment | None		None
label	str | None		None

UnspecifiedEntityLayout dataclass

UnspecifiedEntityLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0
)

Bases: _SimpleMixin, SBGNNode

Class for unspecified entity layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'261213a8-86b2-49ac-a3b8-72af38f2aba5'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node

UnspecifiedEntitySubunit dataclass

UnspecifiedEntitySubunit(
    *,
    id_: str = get_uuid4_as_str(),
    label: str | None = None
)

Bases: Subunit

Class for unspecified entity subunits

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'3a132216-ff1a-4d74-9f62-3456b17191f2'
label	str | None		None

UnspecifiedEntitySubunitLayout dataclass

UnspecifiedEntitySubunitLayout(
    fill: NoneValueType | Color | None = white,
    stroke: NoneValueType | Color | None = black,
    stroke_width: float | None = 1.25,
    *,
    id_: str = get_uuid4_as_str(),
    layout_elements: tuple[LayoutElement] = tuple(),
    group_fill: NoneValueType | Color | None = None,
    group_fill_rule: FillRule | None = None,
    group_filter: NoneValueType | Filter | None = None,
    group_font_family: str | None = None,
    group_font_size: float | None = None,
    group_font_style: FontStyle | None = None,
    group_font_weight: FontWeight | float | None = None,
    group_stroke: NoneValueType | Color | None = None,
    group_stroke_dasharray: tuple[float] | None = None,
    group_stroke_dashoffset: float | None = None,
    group_stroke_width: float | None = None,
    group_text_anchor: TextAnchor | None = None,
    group_transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    filter: NoneValueType | Filter | None = None,
    height: float = 30.0,
    label: TextLayout | None = None,
    position: Point,
    stroke_dasharray: (
        NoneValueType | tuple[float] | None
    ) = None,
    stroke_dashoffset: float | None = None,
    transform: (
        NoneValueType | tuple[Transformation] | None
    ) = None,
    width: float = 60.0
)

Bases: _SimpleMixin, SBGNNode

Class for unspecified entity subunit layouts

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'430f5f99-fe2e-419b-8a83-93495101e787'
layout_elements	tuple[LayoutElement]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	tuple[float] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	float | None	The stroke dashoffset of the group layout	None
group_stroke_width	float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation] | None	The transform of the group layout	None
fill	NoneValueType | Color | None		Color(red=255, green=255, blue=255, alpha=1.0)
filter	NoneValueType | Filter | None	The filter of the node	None
height	float		30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None		Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float] | None	The stroke dasharray of the node	None
stroke_dashoffset	float | None	The stroke dashoffset of the node	None
stroke_width	float | None		1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float		60.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the layout element
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node
childless	Return a copy of the node with no children
children	Return the children of the group layout.
contains	Return true if another layout element is a descendant of the layout element, false otherwise
descendants	Return the descendants of the layout element
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node
east_north_east	Return the east north east anchor of the node
east_south_east	Return the east south east west anchor of the node
equals	Return true if the layout element is equal to another layout element, false otherwise
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children
label_center	Return the label center anchor of the node
north	Return the north anchor of the node
north_east	Return the north east anchor of the node
north_north_east	Return the north north east anchor of the node
north_north_west	Return the north north west anchor of the node
north_west	Return the north west anchor of the node
self_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the self drawing elements of the node
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size of the node
south	Return the south anchor of the node
south_east	Return the south east anchor of the node
south_south_east	Return the south south east anchor of the node
south_south_west	Return the south south west anchor of the node
south_west	Return the south west anchor of the node
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
west	Return the west anchor of the node
west_north_west	Return the west north west anchor of the node
west_south_west	Return the west south west anchor of the node

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node
y	float	Return the y coordinate of the node

anchor_point

anchor_point(anchor_name) -> Point

Return an anchor point of the layout element

Source code in src/momapy/core.py

def anchor_point(self, anchor_name) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle

angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the layout element

Source code in src/momapy/core.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the layout element"""
    bounds = self.to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

border

border(point: Point) -> Point

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node

Source code in src/momapy/core.py

def center(self) -> momapy.geometry.Point:
    """Return the center anchor of the node"""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children

Source code in src/momapy/core.py

def childless(self) -> typing.Self:
    """Return a copy of the node with no children"""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout. These are the self children of the group layout (returned by the self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.
    These are the self children of the group layout (returned by the `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return true if another layout element is a descendant of the layout element, false otherwise

Source code in src/momapy/core.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `true` if another layout element is a descendant of the layout element, `false` otherwise"""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element

Source code in src/momapy/core.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout. The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children

Source code in src/momapy/core.py

def drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the group layout.
    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children
    """
    drawing_elements = self.self_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_group",
        elements=drawing_elements,
        id_=f"{self.id_}_group",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node

Source code in src/momapy/core.py

def east(self) -> momapy.geometry.Point:
    """Return the east anchor of the node"""
    return self.self_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.py

def east_north_east(self) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east west anchor of the node

Source code in src/momapy/core.py

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

equals

equals(other, flattened=False, unordered=False) -> bool

Return true if the layout element is equal to another layout element, false otherwise

Source code in src/momapy/core.py

def equals(self, other, flattened=False, unordered=False) -> bool:
    """Return `true` if the layout element is equal to another layout element, `false` otherwise"""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children

Source code in src/momapy/core.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children"""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node

Source code in src/momapy/core.py

def label_center(self) -> momapy.geometry.Point:
    """Return the label center anchor of the node"""
    return self.position

north

north() -> Point

Return the north anchor of the node

Source code in src/momapy/core.py

def north(self) -> momapy.geometry.Point:
    """Return the north anchor of the node"""
    return self.self_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.py

def north_east(self) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node

Source code in src/momapy/core.py

def north_north_east(self) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, -self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node

Source code in src/momapy/core.py

def north_north_west(self) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.py

def north_west(self) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(
    angle: float,
    unit: Literal["degrees", "radians"] = "degrees",
) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return momapy.drawing.get_drawing_elements_angle(
        drawing_elements=self.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point. When there are multiple intersection points, the one closest to the given point is returned

Source code in src/momapy/core.py

def self_border(
    self, point: momapy.geometry.Point
) -> momapy.geometry.Point:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
    When there are multiple intersection points, the one closest to the given point is returned
    """
    return momapy.drawing.get_drawing_elements_border(
        drawing_elements=self.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label

Source code in src/momapy/core.py

def self_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label"""
    if self.label is not None:
        return [self.label]
    return []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the node

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the node"""
    elements = self._border_drawing_elements()
    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=elements,
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(
        self.drawing_elements()
    )

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

def size(self) -> tuple[float, float]:
    """Return the size of the node"""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node

Source code in src/momapy/core.py

def south(self) -> momapy.geometry.Point:
    """Return the south anchor of the node"""
    return self.self_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.py

def south_east(self) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node

Source code in src/momapy/core.py

def south_south_east(self) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node

Source code in src/momapy/core.py

def south_south_west(self) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 4, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.py

def south_west(self) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 2)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(
    self, to_polygons: bool = False
) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(
            to_polygons=to_polygons
        ).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

def west(self) -> momapy.geometry.Point:
    """Return the west anchor of the node"""
    return self.self_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.py

def west_north_west(self) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() - (self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node

Source code in src/momapy/core.py

def west_south_west(self) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.Line(
        self.center(), self.center() + (-self.width / 2, self.height / 4)
    )
    angle = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node

y property

y: float

Return the y coordinate of the node